Resource
| Id | Histone_ChIP-seq/ENCSR527BFF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR527BFF [biosample_summary="Homo sapiens stomach tissue male adult (34 years)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN737RFM|/analyses/ENCAN737RFM/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF017GGC|/files/ENCFF017GGC/} processed by ChIP-seq ENCODE3 hg19 pipeline has 13775361 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF017GGC|/files/ENCFF017GGC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.86. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed alignments file {ENCFF017GGC|/files/ENCFF017GGC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.50. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR527BFF | float |
Histone_ChIP-seq_ENCSR527BFF |
Histone_ChIP-seq ENCSR527BFF [biosample_summary="Homo sapiens stomach tissue male adult (34 years)" and target="H3K27me3"]
|
 |
[1.84, 7.51] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 388650 | 0.01% | 1239 |
| chr1 | 32630 | 0.01% | 103 |
| chr2 | 38056 | 0.02% | 118 |
| chr3 | 20018 | 0.01% | 67 |
| chr4 | 13887 | 0.01% | 46 |
| chr5 | 22023 | 0.01% | 72 |
| chr6 | 21132 | 0.01% | 58 |
| chr7 | 15264 | 0.01% | 50 |
| chr8 | 19098 | 0.01% | 59 |
| chr9 | 12792 | 0.01% | 41 |
| chr10 | 25282 | 0.02% | 76 |
| chr11 | 19402 | 0.01% | 67 |
| chr12 | 20430 | 0.02% | 73 |
| chr13 | 12722 | 0.01% | 41 |
| chr14 | 12673 | 0.01% | 41 |
| chr15 | 11822 | 0.01% | 42 |
| chr16 | 16161 | 0.02% | 53 |
| chr17 | 19772 | 0.02% | 63 |
| chr18 | 9885 | 0.01% | 32 |
| chr19 | 8972 | 0.02% | 30 |
| chr20 | 14916 | 0.02% | 50 |
| chr21 | 7049 | 0.02% | 16 |
| chr22 | 8322 | 0.02% | 26 |
| chrM | 2264 | 13.66% | 4 |
| chrX | 3015 | <0.01% | 8 |
| chrY | 1063 | <0.01% | 3 |
| 3341 contigs with no values (129060516 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 1239 | 185 | 2192 | 313.68 | 285 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF653SWP.bed.gz | 25.69 KB | 13a24c6dfde0f6a2fcba9ff84662a53a |
| ENCFF653SWP.tabix.bed.gz | 13.37 KB | 1e92a22dd77d27ba27bbf53c54ad9eb1 |
| ENCFF653SWP.tabix.bed.gz.tbi | 17.04 KB | 881a2fa8f1c3a7eeabe4205f2d812b5d |
| genomic_resource.yaml | 3.22 KB | 64134e149d909680c211a5c577c7fa35 |
| statistics/ |